Shanahan explained his reasoning after the 43-17 defeat that left the 49ers still winless at home.
"Just because of how down we were (with the cornerback numbers) going into the game," Shanahan told reporters. "We got him off of practice squad this week with the injuries that we had. (Ken) Webster was his backup."
Ahkello Witherspoon eventually replaced Allen, but much of the damage had already been done.
"Ahkello, he tried to go this week," Shanahan continued, "but he was too tight to go throughout practice this week. Because of our low numbers, we still dressed him for emergency. So we were trying to hold out, see how long we could go through with that, and when Ahkello came up to us on the sideline and said he wanted to go and wanted a shot, it gave us a little more confidence with his hamstring.
"He went in, was able to pull it off, and get out of the game without tearing it," Shanahan added. "That was the decision on it."
Witherspoon was limited all week during practices. The 49ers entered the game with two cornerbacks — Dontae Johnson (groin) and Emmanuel Moseley (concussion) — inactive due to injuries. K'Waun Williams landed on injured reserve this weekend, and Richard Sherman wasn't ready to return.
"We thought it would take two injuries to [play Witherspoon]," Shanahan said. "Obviously, with Allen struggling a little bit, we were going to go with Webster. That was the plan going in, but Ahkello went up to the defensive staff, I want to say sometime in the second quarter, and told them he felt good, was ready to go. He wanted to go in for the challenge.
"At that time, I was very happy to hear that, so we threw him out there. I know he didn't feel great battling through that, but he definitely helped us in going out there."
Shanahan added that Moseley recently saw a specialist regarding his concussion, and the coach hopes his starting cornerback can return sometime this week. Sherman could also potentially start practicing again this week too.
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